Some examples of CALANGO output are available under docs/articles/results in the CALANGO Github repository, and their output pages are linked below.

• Example 1 relates to the case study “Homologous regions and biological roles associated with prophage density in pathogenic and free-living Escherichia coli”.
• Example 2 relates to the case study Homologous regions associated with maximum height in Angiosperms.

Both examples are presented as part of the manuscript CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species. Please navigate to one of the links below to check the examples:

These examples can be independently reproduced by running the script below. After running CALANGO::retrieve_data_files(), the main input files (which can be used as templates for other studies) will be located under subfolder /parameters.

install.packages("CALANGO")
library(CALANGO)

# Change target.dir to save under a different folder if needed
target.dir <- "data"

# Change to increase number of cores.
ncores <- 1

CALANGO::retrieve_data_files(target.dir)

# Get CALANGO input files for the examples
inputfiles <- dir(paste0(target.dir, "/parameters"), full.names = TRUE)

# run for all example files
for (i in seq_along(inputfiles)){
cat("\nProcessing example", i, "of", length(inputfiles), "\n")
defs <- CALANGO::run_CALANGO(inputfiles[i], cores = ncores)
}